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1 Taxonomic changes of the genera Staphylococcus and Streptococcus on this decade Follow-up information Yoshiaki KAWAMURA S rrna Bergey s manual of Systematic Bacteriology 2 Bergey s manual 3 The Firmicutes whole genome sequence Bergey s manual DNA-DNA 70 Tm S rrna 16S rrna 97 DNA-DNA 3 16S rrna DNA- DNA 16S rrna DNA-DNA S rrna DNA-DNA Microbiology Today SGM IJSEMInternational Journal of Systematic and Evolutionary Microbiology Department of Microbiology Aichi Gakuin University, School of Pharmacy (1-100 kusumoto- cho, Nagoya)
2 16S rrna DNA-DNA 16S rrna DNA-DNA Microplate Ezaki et al., Tourova & Antonov, De Lay et al., dot hybridization Amakata et al., S rrna Stackebrandt & Ebers, Microbiology Today ; , 2006 Bergey s manual The Archaea and the deeply branching and phototrophic Bacteria The Proteobacteria The Firmicutes The Bacteroidetes, Spirochaetes, Tenericutes Mollicutes, The Actinobacteria S rrna Taxonomic outline of the Archaea and BacteriaThe road map of the Manual Revised Road Map to the Phylum Firmicutes 6 Mollicutes Firmicutes Tenericutes Bergey s manual 4 Tenericutes Mollicutes clostridia Firmicutes 16S rrna Firmicutes Mollicutes Tenericutes Mollicutes Family Erysipelothrichaceae Erysipelotrichia Erysipelotrichales Bergey s manual 3 DNA GC mol Firmicutes 3 Bacilli, Clostridia, Eryshipelotrichia Bacilli Bacillales Staphylococcaceae
3 Bacilli Lactobacillaceae Streptococcaceae Abiotrophia Granulicatella Aerococcaceae Carnobacteriaceae 7 9 Phylum Firmicutes Phylum Firmicutes Class Bacilli Order Bacillales Family Bacillaceae Family Listeriaceae Family Staphylococcaceae Genus Staphylococcus Genus Jeotigalicoccus Genus Macrococcus Genus Salinicoccus Order Lactobacillaceae Family Lactobaci ; llaceae Family Aerococcaceae Family Carnobacteriaceae Family Enterococcaceae Family Leuconostocaceae Family Streptococcaceae Genus Streptococcus Genus Lactococcus Genus Lactovum Class Clostridia Order Clostridiales Family Clostridiaceae Family Eubacteriaceae Family Peptococcaceae Family Peptostreptococcaceae Family Ruminococcaceae Family Veillonellaceae Class Erysipelotrichia Order Erysipelotrichales Family Erysipelothrichaceae Bergey s manual of systematic bacteriology 2nd edition, Vol Bergey s manual 3 Genus Staphylococcus 7 Staphylococcus succinus subsp. succinus position 3 meso- m-dpm m-dpm 1 9 Bergey s manual S. epidermidis, S. haemolyticus, S. saporphyticus lysozyme DNARNA lysostaphin achromopeptidase labiase 10 house keeping gene S. pseudintermedius S. simiae S. pettenkoferi S. devriesei S. massiliensis S. microti S. rostri S. agnetis S. stepanovicii 2005 Staphylococcus mec 4COAG : clump : COAG :, clump : 4 COAG : d, clump :
4 16S rrna, rpobbeta subunit of RNA polymerase, tufelongation factor EF-Tu, dnajheat shock protein Hsp40, hsp6060kda heat shock protein, sodasuperoxide dismutase 6 11 soda dnaj 2 16S rrna N-GlcNAc N-MurNAc 4 postion1 4 position3 L- L S. succinus subsp. succinus position3 meso - meso Corynebacterium MAXMINMedian
5 dnaj DNA-DNA hybridizationkloos 12 16S rrna Takahashi 13 hsp60 Kwok 14 dnaj Shah 15 aureus group hyicus-intermedius group saporphyticus group sciuri group sciuri group Whole genome sequence S. aureus S. epidermidis, S. lugdunensis, S. pseudointermedius 2 S. carnosus, S. haemolyticus, S. saporphyticus 1 saprophyticus NOV-R simulans S carnosus subsp utilis S carnosus subsp carnosus S gallinarum S cohnii subsp urealyticus S cohnii subsp cohnii S saprophyticus subsp saprophyticus S saprophyticus subsp bovis S xylosus S succinus subsp casei S succinus subsp succinus S equorum subsp linens S equorum subsp equorum S auricularis S pettenkoferi S simulans S piscifermentans S condimenti S arlettae S kloosii S caprae S saccharolyticus S capitis subsp urealyticus S capitis subsp capitis epidermidis S epidermidis S warneri S pasteuri S aureus subsp anaerobius S aureus subsp aureus S simiae S hominis subsp hominis S hominis subsp novobiosepticum S haemolyticus S devriesei S lugdunensis S delphini S pseudintermedius S intermedius aureus COAG haemolyticus Bacillus subtilis (out group) sciuri NOV-R OXI S stepanovicii S lentus S vitulinus S fleurettii S sciuri subsp sciuri S sciuri subsp carnaticus S sciuri subsp rodentium S felis S rostri S muscae S microti S hyicus S lutrae S schleiferi subsp schleiferi S schleiferi subsp coagulans S chromogenes hyicusintermedius COAG NOV-ROXICOAG
6 S. arlettae S. aureus S.capitis S. caprae S. carnosus subsp. carnosus S. epidermidis S. haemolyticus S. hominis S. lugudunensis S. massiliensis S. pseudointermedius S. saporphyticus S. simiae S. warneri Staphylococcus sp. OJ82 Total or Average 1 Mbp 10, , , , , , , , , , , , , , , , 70 1 : 2 : Integrated Microbial Genomes ,518 2,7592,202 3,089 2,292 2,472 2, ,314 2,704 2,809 2,2442,238 2,249 2,5272,488 2,570 2,467 2,4822,435 2,528 2,637 2,648 2,439 2,912 2, Mb Mb, IJSEM pyogenic group 4 8 mitis group 3 anginosus group 2 8 others new species group S rrna 19 6 pyogenic, mitis, salivarius, mutans, bovis, anginosus group 7 S. pleomorphus Clostridium Bergey s manual Species Incertae Sedis bovis group Dr. Killian house keeping gene MLSAMulti Locus Sequence Analysis2009 α mitis group anginosus group salivarius group 2012 pyogenic group S. dysgalactiae, S. pyogenes, S. canis, S. equi 2013 anginosus group 2 S. constellatus subsp. viborgensis subsp. whileyi 1999 Dr. Whiley S. constellatus subsp. pharyngis DNA-group2 20
7 1 genomosubspeciesaj1 Dr. Killina 7 house keeping gene mapmethionine aminopeptidase, pflpyruvate formate lyase, ppac inorganic pyrophosphatase, pyk pyruvate kinase, rpobrna polymerase beta subunit, sodasuperoxide dismutase, tufelongation factor Tu rpob 21 S. suis S. suis Lancefield R, S, T DNA-group D Lancefield R 2 MLST ST complex-1 25, 26 2 S. suis pulsotypes 2006 Streptococcus 1 2 Lancefiled pyogenic group pyogenic group mitis group mitis group mitis group? S. massiliensis S. ictaluri S. pseudoporcinus S. orisuis S. caballi S. henryi S. dentirousetti S. merionis S. plurextorum S. dentapri S. porci S. ursoris S. lactarius S. rupicaprae S. porcorum S. tigurinus S. troglodytidis S. troglodytae S. danieliae G D D B B D B pyogenic group pyogenic group anginosus group anginosus group S. orisasini 3 S. dentasini 3 S. honkongensis 3 S. fryi 3 subsp. whileyi 3 S. constellatus subsp. viborgensis 3 M C C IJSEM Validation List MLSA 1999 S. intermedius S. constellatus subsp. constellatus S. constellatus subsp. pharyngitis DNA group 2 1 MLSA-cluster Cluster-1 Cluster-2 Cluster-3 Cluster-4 Cluster-5 Cluster-6 Cluster DNA group 2 S. intermedius S. constellatus subsp. constellatus S. constellatus subsp. pharyngitis S. constellatus subsp. viborgensis genomespecies AJ1 subsp. anginosus subsp. whileyi
8 Lancefield antigen A B C D E F G H K L M N O P Q R S T U V Lancefield Species S. pyogenes S. castoreus S. dysgalactiae subsp. equisimilis S. orisratti S. constellatus subsp. constellatus S. agalactiae S. halichoeri S. plurextorum S. porci S. troglodytidis S. equi subsp. equi S. equi subsp. zooepidemicus S. equi subsp. ruminatorum S. dysgalactiae subsp. dysgalactiae S. dysgalactiae subsp. equisimilis S. phocae S. marimammalium S. parasanguinis subsp. whileyi 2 S. constellatus subsp. constellatus S. constellatus subsp. pharyngitis S. constellatus subsp. viborgensis 2 S. bovis S. equinus S. alactolyticus S. infantarius subsp. infantarius S. infantarius subsp. coli S. lutetiensis S. gallolyticus subsp. gallolyticus S. gallolyticus subsp. macedonicus S. gallolyticus subsp. pasteurinus S. henryi S. merionis S. rupicaprae Enterococci S. porcinus S. uberis S. parauberis S. mutans S. phocae S. parasanguinis S. constellatus subsp. constellatus S. dysgalactiae subsp. equisimilis S. canis S. parasanguinis S. massiliensis S.gordonii S. sanguinis S. mitis S. salivarius S. dysgalactiae subsp. dysgalactiae S. fryi 2 Lactococci S. mitis S. uberis S. parauberis S. porcinus Enterococci S. suis S. suis S. suis S. porcinus S. porcinus Isolated from Group 1 Mutans group Mitis?or anginosus? Mutans group Mutans group Salivarius group 116S rrna IJSEM
9 27 32, 33, 34 16S rrna 28 S. suis 2005 S. suis ST S. suis S. suis α S. gordonii, S. sanguinis, S. parasanguinis 32 R Lancefield A V I, J M M S. fryi 33 Lancefield M 3 34 S. fryi Biovar-II α Biovar-I S. fryi Biovar-III Biovar-I 1 16S rrna mitis group Biovar-III S. agalactiae 35 Whole genome sequence complete sequ- S. agalactiae S. dysgalactiae subsp. equisimilis S. equi subsp. equi S. equi subsp. zooepidemicus S. gallolyticus subsp. gallolyticus S. gordonii S. infantarius subsp. infantarius S. infantis S. mitis S. mutans S. oralis S. parasanguinis S. parauberis S. pasteurianus S. pneumoniae S. pseudopneumoniae S. pseudoporcinus S. pyogenes S. salivarius S. sanguinis S. suis S. thermophilus S. uberis S. vestibularis Streptococcus sp. Other 25 species 3 Total or Average 1 115, 6 40, 4 33, 0 11, 0 33, 0 43, 1 11, 0 22, 0 30, 3 71, 6 43, 1 31, 2 42, 2 21, 1 11, , 43 21, 1 20, , 1 53, 2 31, , 2 66, 0 11, 0 20, 2 110, , , 118 Mbp ,2451,737 2,685 1,9451,831 2,074 2,1942,128 2,287 2,095 2,0451,961 2,159 2,3422,255 2,430 2,149 2,0792,045 2,113 1,9811,831 2,132 1,8591,724 2,095 1,9861,952 2,059 1,9001,826 1,989 2,0942,061 2,119 2,0801,937 2,222 1,944 2,2401,850 2,846 2,2382,196 2,280 2,0882,072 2,104 1,9341,735 2,091 1,9661,594 2,113 2,2442,052 2,367 2,0541,607 2,276 2,0171,820 2,230 1,843 1,9881,920 2,056 1,9761,826 2,169 1,508 2,529 2,086 1 : 2 : 3 : 1 25 S. australis, S. bovis, S. caballi, S. constellatus subsp. pharyngis, S. criceti, S. cristatus, S. didelphis, S. downei, S. entericus, S. equinus, S. ferus, S. henryi, S. ictaluri, S. intermedius, S. macacae, S. marimammalium, S. massiliensis, S. merionis, S. minor, S. orisratti, S. ovis, S. peroris, S. porcinus, S. thoraltensis, S. urinalis. Integrated Microbial Genomes
10 ence S. pneumoniae. S. pyogenes S. suis 2005 outbreak Mbp House keeping gene MLST 7 10Kbp Mbp 0.5 DNA-DNA hybridization high through put : , Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LM, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, and Truper HG.: Report of the ac hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Sys. Bacteriol. : , Stackebrandt E, Goebel BM.: Taxonomic note ; A place for DNA-DNA reassociation and 16S rrna sequen-ce analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. : , Stackebrandt E and Ebers J.: Taxonomic parameters revisited : tarnished gold standards. Micobiology Today. : , Garrity GM and Holt JG.: The road map to the manual , In Bergery s manual of systematic bacteriology 2nd edition, vol.1. Garrity GMeds. NewYork, Springer-Verlag. 6 Ludwig W, Schleifer KH and Whitman WB.: Revised road map to the phylum Firmicutes. 1-13, Berge-ry s manual of systematic bacteriology 2nd edition, vol.3. In Parte ACeds. NewYork, Springer-Verlag. 7 Schleifer KH and Bell J.: Genus I Staphylococcus , In Bergery s manual of systematic bacteriology 2nd edition, vol.3. Parte ACeds. NewYork, Springer-Verlag. 8 Lambert LH, Cox T, Mitchell K, Rosselló-Mora RA, Del Cueto C, Dodge DE, Orkand P, Cano RJ.: Staphylococcus succinus sp. nov., isolated from Dominican amber. Int J Syst Bacteriol. : , Lambert LH, Cox T, Mitchell K, Rosselló-Mora RA, Del Cueto C, Dodge DE, Orkand P, Cano RJ.: ERRAT. Staphylococcus succinus sp. nov., isolated from Dominican amber. Int J Syst Bacteriol. : 933, Niwa T, Kawamura Y, Katagiri Y, Ezaki T.: Lytic enzyme, labiase for a broad range of Gram-positive bacteria and its application to analyze functional DNARNA. J Microbiol Methods. : , La Scola B, Zeaiter Z, Khamis A, Raoult D.: Genesequence-based criteria for species definition in bacteriology : the Bartonella paradigm. Trends Microbiol. : , Kloos WE, Schleifer KH. & Götz F.: The genus Staphylococcus. In The Prokaryotes, 2nd edn , Balows A, Truper HG, Dworkin M, Harder W and Schleifer KHeds. New York : Springer. 13Takahashi T, Satoh I, and Kikuchi N.: Phylogenetic relationships of 38 taxa of the genus Staphylococcus based on 16S rrna gene sequence analysis. Int. J. Syst. Bacteriol. : , Kwok AY and Chow AW.: Phylogenetic study of Staphylococcus and Macrococcus species based on partial hsp60 gene sequences. Int J Syst Evol Microbiol : 87-92, Shah MM, Iihara H, Noda M, Song SX, Nhung PH, Ohkusu K, Kawamura Y, Ezaki T.: dnaj gene sequencebased assay for species identification and phylogenetic grouping in the genus Staphylococcus Int J Syst Evol Microbiol. : 25-30, Shukla SK, Pantrangi M, Stahl B, Briska AM, Stemper ME, Wagner TK, Zentz EB, Callister SM, Lovrich SD, Henkhaus JK, Dykes CW.: Comparative whole-genome mapping to determine Staphylococcus aureus genome size, virulence motifs, and clonality. J Clin Microbiol. : , Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP and Spratt BG.: Assigning strains to bacterial species
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51 12 2005313 Taxonomic changes of the genera Staphylococcus and Streptococcus on this decade. Yoshiaki KAWAMURA Staphylococcus aureus, Staphylococcus epidermidis MRSA MRSE Streptococcus pyogenes, Streptococcus
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